help > Overlay not showing up
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Sep 13, 2022 11:09 AM | overlayquestio
Overlay not showing up
Hi,
I have been working with PET imaging and I have tried to visualize some parameters with MRIcroGL.
Whenever i try to overlay an image (nifti) over an MRI template, the overlay does not show up and the colorbar ranges from 0 to 1.
If I just open the same nifti file without it being an overlay it works fine.
How can I fix this problem so I can overlay my nifti files on top of a MRI template?
Kind regards
I have been working with PET imaging and I have tried to visualize some parameters with MRIcroGL.
Whenever i try to overlay an image (nifti) over an MRI template, the overlay does not show up and the colorbar ranges from 0 to 1.
If I just open the same nifti file without it being an overlay it works fine.
How can I fix this problem so I can overlay my nifti files on top of a MRI template?
Kind regards
Sep 13, 2022 01:09 PM | Chris Rorden
RE: Overlay not showing up
You need to spatially normalize the PET image to match the space of
the template image. You can use FSL, ANTS, AFNI, or SPM to
normalize you image. For MRI scanners, the initial origin of the
image is the magnet isocenter, which is typicaly inside the head
for brain scans. For CT (and I presume PET) the origin for DICOM is
the table center, which is often a meter away from the head.
Sep 13, 2022 01:09 PM | overlayquestio
RE: Overlay not showing up
Thank you for the quick response.
I forgot to mention that the preprocessing for the Nifti files are all done.
If i load the template and the Nifti file in PMOD for example, everything is aligned.
Could there be another reason for this problem?
I appreciate the help.
I forgot to mention that the preprocessing for the Nifti files are all done.
If i load the template and the Nifti file in PMOD for example, everything is aligned.
Could there be another reason for this problem?
I appreciate the help.
Sep 13, 2022 01:09 PM | Chris Rorden
RE: Overlay not showing up
1. Can you share your sample datasets with my institutional email:
https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php
2. PMOD is proprietary software, so without seeing the images I can only speculate. However, I am going to go out on a limb here and suggest that they do not implement the NIfTI format correctly, e.g. either ignoring the SForm or giving the QForm precedence over the SForm.
3. PMOD is professional software. They have an obligation to support their users. I suggest you contact them and ask them why their software is incompatible with open tools like SPM, FSL and MRIcroGL.
https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php
2. PMOD is proprietary software, so without seeing the images I can only speculate. However, I am going to go out on a limb here and suggest that they do not implement the NIfTI format correctly, e.g. either ignoring the SForm or giving the QForm precedence over the SForm.
3. PMOD is professional software. They have an obligation to support their users. I suggest you contact them and ask them why their software is incompatible with open tools like SPM, FSL and MRIcroGL.